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Detailed information for vg1107498561:

Variant ID: vg1107498561 (JBrowse)Variation Type: SNP
Chromosome: chr11Position: 7498561
Reference Allele: TAlternative Allele: C
Primary Allele: CSecondary Allele: T

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:


TACACACACAAACTTCCAACTTTTCCGTCAAATCATTCTAATTTTTTCAAACTTCCAATTTTAACGTGGAACTAAACACGGCCTAAGTAGGGAACAATTC[T/C]
CACCGAACACAGCAGCTACTCCCTCCGTCCCATTTTAAACACAGTTATGACTTTCCGTATTCAATTTTGATCGTGTGTCGTATTTGAAACTTTTTATAAT

Reverse complement sequence

ATTATAAAAAGTTTCAAATACGACACACGATCAAAATTGAATACGGAAAGTCATAACTGTGTTTAAAATGGGACGGAGGGAGTAGCTGCTGTGTTCGGTG[A/G]
GAATTGTTCCCTACTTAGGCCGTGTTTAGTTCCACGTTAAAATTGGAAGTTTGAAAAAATTAGAATGATTTGACGGAAAAGTTGGAAGTTTGTGTGTGTA

Allele Frequencies:

Populations Population SizeFrequency of C(primary allele) Frequency of T(secondary allele) Frequency of N Frequency of DEL Frequency of others Allele
All  4726 89.00% 10.90% 0.02% 0.00% NA
All Indica  2759 99.60% 0.40% 0.00% 0.00% NA
All Japonica  1512 72.00% 28.00% 0.00% 0.00% NA
Aus  269 99.60% 0.40% 0.00% 0.00% NA
Indica I  595 99.50% 0.50% 0.00% 0.00% NA
Indica II  465 100.00% 0.00% 0.00% 0.00% NA
Indica III  913 100.00% 0.00% 0.00% 0.00% NA
Indica Intermediate  786 98.90% 1.10% 0.00% 0.00% NA
Temperate Japonica  767 66.40% 33.60% 0.00% 0.00% NA
Tropical Japonica  504 85.50% 14.50% 0.00% 0.00% NA
Japonica Intermediate  241 61.40% 38.60% 0.00% 0.00% NA
VI/Aromatic  96 29.20% 70.80% 0.00% 0.00% NA
Intermediate  90 85.60% 13.30% 1.11% 0.00% NA

Allele Effect:

Var ID Var Locus snpEff Annotation CooVar Annotation Chromatin Accessibility Score PolyPhen-2 Effect PolyPhen-2 Score SIFT Effect SIFT Score
vg1107498561 T -> C LOC_Os11g13670.1 upstream_gene_variant ; 3100.0bp to feature; MODIFIER silent_mutation Average:50.592; most accessible tissue: Minghui63 panicle, score: 82.128 N N N N
vg1107498561 T -> C LOC_Os11g13680.1 downstream_gene_variant ; 3867.0bp to feature; MODIFIER silent_mutation Average:50.592; most accessible tissue: Minghui63 panicle, score: 82.128 N N N N
vg1107498561 T -> C LOC_Os11g13670-LOC_Os11g13680 intergenic_region ; MODIFIER silent_mutation Average:50.592; most accessible tissue: Minghui63 panicle, score: 82.128 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg1107498561 6.05E-06 6.05E-06 mr1244 Jap_All Not Genome-wide association analyses provide genetic and biochemical insights into natural variation in rice metabolism, Nat Genet, 46(7):714-21, PMID:24908251
vg1107498561 5.09E-06 5.09E-06 mr1589 Jap_All Not Genome-wide association analyses provide genetic and biochemical insights into natural variation in rice metabolism, Nat Genet, 46(7):714-21, PMID:24908251
vg1107498561 1.19E-06 1.19E-06 mr1918 Jap_All YES Genome-wide association analyses provide genetic and biochemical insights into natural variation in rice metabolism, Nat Genet, 46(7):714-21, PMID:24908251
vg1107498561 NA 1.34E-06 mr1961 Jap_All Not Genome-wide association analyses provide genetic and biochemical insights into natural variation in rice metabolism, Nat Genet, 46(7):714-21, PMID:24908251